The Human Phenotype Ontology: Accelerating Computational Integration of Clinical Data for Genomics

人类表型本体论：加速基因组学临床数据的计算整合

• 批准号: 10681348
• 负责人: MELISSA A HAENDEL
• 金额: $ 73.86万
• 依托单位: JACKSON LABORATORY
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-20 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10681348
• 关键词: Academia; Acceleration; Address; Adopted; Adoption; Age of Onset; Algorithms; Automated Annotation; Basic Science; Biology; Cardiology; Case Study; Classification; Clinic; Clinical; Clinical Data; Clinical Management; Clinical Medicine; Collaborations; Communities; Computational algorithm; Computer Analysis; Computer software; Data; Data Reporting; Development; Diagnosis; Diagnostic; Differential Diagnosis; Discipline; Disease; Disease model; Disparate; Electronic Health Record; Ensure; Event; Face; Foundations; Frequencies; Genes; Genetic Diseases; Genome; Genomics; Goals; Guidelines; Health; Human; Immunology; Industry; International; Intervention; Laboratories; Language; Link; Location; Maintenance; Malignant Childhood Neoplasm; Manuals; Maps; Medical; Medical Genetics; Modeling; Modernization; Nature; Nephrology; Neurology; Online Systems; Ontology; Ophthalmology; Patients; Performance; Pharmacogenomics; Phenotype; Process; Publishing; Rare Diseases; Research; Resources; Seizures; Sex Bias; Standardization; Structure; Terminology; Text; Time; Translations; Variant; biobank; bioinformatics resource; biomedical ontology; causal variant; clinical care; clinical decision-making; cohort; cost effective; data exchange; diagnostic tool; disease natural history; disease phenotype; experience; genetic variant; genomic data; genomic variation; health care delivery; human disease; improved; interoperability; ontology development; patient registry; phenotypic data; precision medicine; programs; quality assurance; user-friendly; variant of unknown significance; web portal

PROJECT SUMMARY/ABSTRACT To improve diagnostic yield for rare diseases, we developed the Human Phenotype Ontology (HPO) in 2008 as a comprehensive bioinformatic resource that provides a standardized terminology of phenotypic abnormalities for the analysis of human diseases. HPO reduces ambiguity in disease descriptions—thus enabling more robust differential diagnosis and clinical care—and enables phenotypic contextualization of genomic data for diagnostics and precision medicine. The performance of computational algorithms for differential diagnostics with HPO terms depends critically on the comprehensiveness and depth of HPO annotations for diseases. However, the current manual nature of our biocuration process has limited the quality, depth, and coverage of these annotations. Therefore, this proposal's objectives are to greatly expand the corpus of disease-phenotype annotations by automating portions of the curation and expanding the computational disease model. This project, HPO: Accelerating Computational Integration of Clinical Data for Genomics, will maintain and advance HPO resources to address the needs of a growing number of medical disciplines that have adopted the HPO. We will achieve this goal by 1) automating HPO development, maintenance, and release processes, 2) developing representations of rare disease treatments and interventions, and 3) extending our current computational disease models to represent time course, sex biases, and frequency of events, and to incorporate case report data. We also provide a sustainable solution to community contribution with a user-friendly, web- based portal to enable contributors to vet and suggest improvements to the ontology and the annotations and grow the HPO contributor community. In summary, our project addresses the most pressing needs for advancements of the HPO to ensure sustainable, robust, and rigorous development, to enable HPO resources to support new communities, new applications, and more medical disciplines.

项目概要/摘要 为了提高罕见疾病的诊断率，我们于 2008 年开发了人类表型本体 (HPO)： 全面的生物信息资源，提供表型异常的标准化术语 HPO 可以减少疾病描述中的歧义，从而使疾病描述更加稳健。 鉴别诊断和临床护理，并实现基因组数据的表型背景化 诊断和精准医学。 使用 HPO 项进行差分诊断的计算算法的性能关键取决于 HPO 疾病注释的全面性和深度 然而，我们目前的手动性质。 生物管理过程限制了这些注释的质量、深度和覆盖范围，因此，该提案的。 目标是通过自动化部分内容来极大地扩展疾病表型注释的语料库 管理和扩展计算疾病模型。 该项目，HPO：加速基因组学临床数据的计算集成，将维护和 HPO 资源可满足越来越多采用该技术的医学学科的预先需求 HPO。我们将通过 1) 自动化 HPO 开发、维护和发布流程来实现这一目标，2) 开发罕见疾病治疗和干预措施的代表性，以及 3）扩展我们目前的 计算疾病模型来表示时间过程、性别偏见和事件频率，并纳入 我们还通过用户友好的网络贡献提供可持续的解决方案。 基于门户，使贡献者能够审查本体和注释并提出改进建议 发展 HPO 贡献者社区。 总之，我们的项目解决了 HPO 进步的最紧迫需求，以确保可持续、 稳健、严格的开发，使 HPO 资源能够支持新社区、新应用程序和 更多医学学科。

项目成果

Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity.

针对先天性免疫缺陷的定义群体的人类表型本体论的管理和扩展。

• 发表时间: 2022-01
• 作者: Haimel, Matthias;Pazmandi, Julia;Heredia, Raúl Jiménez;Dmytrus, Jasmin;Bal, Sevgi Köstel;Zoghi, Samaneh;van Daele, Paul;Briggs, Tracy A;Wouters, Carine;Bader;Aeschlimann, Florence A;Caorsi, Roberta;Eleftheriou, Despina;Hoppe
• 通讯作者: Hoppe

[Rare-disease data standards].

[罕见疾病数据标准]。

• 发表时间: 2022-11
• 作者: Robinson, Peter N;Graessner, Holm
• 通讯作者: Graessner, Holm

Diffuse alveolar hemorrhage in children with interstitial lung disease: Determine etiologies!

间质性肺疾病儿童弥漫性肺泡出血：确定病因！

• 发表时间: 2023-04
• 影响因子: 3.1
• 作者: Knoflach, Katrin;Rapp, Christina Katharina;Schwerk, Nicolaus;Carlens, Julia;Wetzke, Martin;Emiralioğlu, Nagehan;Kiper, Nural;Ring, Astrid Madsen;Buchvald, Frederik;Manali, Effrosyni;Papiris, Spyros;Reu;Kappler, Matthias;Schieber
• 通讯作者: Schieber

Inherited deletion of 9p22.3-p24.3 and duplication of 18p11.31-p11.32 associated with neurodevelopmental delay: Phenotypic matching of involved genes.

与神经发育迟缓相关的 9p22.3-p24.3 遗传性缺失和 18p11.31-p11.32 重复：相关基因的表型匹配。

• 发表时间: 2023-02
• 影响因子: 5.3
• 作者: Ajami, Naser;Kerachian, Mohammad Amin;Toosi, Mehran Beiraghi;Ashrafzadeh, Farah;Hosseini, Susan;Robinson, Peter N;Abbaszadegan, Mohammad Reza
• 通讯作者: Abbaszadegan, Mohammad Reza

Supplementation of the ESID registry working definitions for the clinical diagnosis of inborn errors of immunity with encoded human phenotype ontology (HPO) terms.

使用编码的人类表型本体 (HPO) 术语补充了 ESID 注册表工作定义，用于先天性免疫缺陷的临床诊断。

• 发表时间: 2020
• 作者: Gasteiger, Lukas M;Robinson, Peter N;Pazmandi, Julia;Boztug, Kaan;Seppänen, Mikko R J;Seidel, Markus G;Registry Working Party of the European Society for Immunodeficiencies (ESID)
• 通讯作者: Registry Working Party of the European Society for Immunodeficiencies (ESID)